I was going for a pacifist playthrough, and so I used the tranquilizer rifle and stun gun almost exclusively.
During the Cloak & Daggers side-mission, I was aiming to incapacitate Double-T, with the first obstacle being the henchman sitting on the couch outside his apartment door. I took out my stun-gun and made short work of him, but as I was dragging him away from where he collapsed I noticed that he appeared to be dead:

This is the first time I've had someone die after shooting him with the stun gun. Just to try it out, I reloaded and shot him with the tranquilizer rifle, only to have him die again (maybe he has a severe allergy to being unconscious).
So, is this just some sort of weird glitch, or does this actually count as a kill, thus disqualifying me for the pacifist achievement?